Helicase Mutations in United States Isolates of SARS-CoV-2 Altered Protein Stability and Binding Dynamics

Abstract

Severe Acute Respiratory Syndrome Coronavirus-2, which causes Coronavirus 2019, has resulted in the deaths of more than 7 million people. The helicase, encoded by non-structural protein-13 in the virus genome, plays a critical role in the virus's life cycle and is at the heart of treatment approaches. The study revealed the impact of helicase protein mutations on protein stability and nucleic acid binding dynamics in United States SARS-CoV-2 isolates. Nine recurrent mutations exceeding the predefined occurrence threshold were identified and subjected to structural modeling, protein stability prediction, and helicase–nucleic acid docking analysis. Utilizing data from nine mutations (Ser36Pro, Thr127Asn, His164Tyr, Met233Ile, Tyr324Cys, Ala368Val, Ala389Val, Arg392Cys, Thr599Ile) identified from isolates, mutant protein models were generated using deep learning algorithms. Protein stability alterations were assessed using SDM2, mCSM, DUET, and DynaMut2 tools. The helicase-nucleic acid interaction was evaluated through molecular docking analysis. Consensus-based stability prediction indicated that several mutations were predicted to reduce nsp13 stability, whereas His164Tyr was consistently predicted to have a stabilizing effect across all four tools. Some substitutions, including Met233Ile and Thr599Ile, showed method-dependent effects. Molecular docking analysis suggested that the recurrent mutation set may alter helicase–RNA interface energetics and spatial arrangement. However, these docking-derived changes should be interpreted as computational estimates rather than direct evidence of increased nucleic acid-binding affinity. The concurrent occurrence of reduced predicted protein stability and more favorable docking-derived nucleic acid interface scores suggests that these mutations may influence helicase–nucleic acid recognition; however, direct effects on viral replication kinetics require experimental validation.

Keywords

• SARS-CoV-2
• Helicase
• Mutation
• Protein stability
• Binding dynamics

Supporting Institution

Malatya Turgut Ozal University Scientific Research Projects Coordination Unit

Project Number

2022/13

Ethical Statement

It's not necessary.

Thanks

This work has been supported by Malatya Turgut Ozal University Scientific Research Projects Coordination Unit under grant number 2022/13.

Amerikan kaynaklı SARS-CoV-2 suşlarında helikaz mutasyonları protein stabilitesini ve bağlanma dinamiklerini değiştirdi.

Abstract

Şiddetli Akut Solunum Sendromu Koronavirüs-2 (SARS-CoV-2), 2019 Koronavirüsüne neden olarak 7 milyondan fazla insanın ölümüne yol açmıştır. Virüs genomunda yapısal olmayan protein-13 tarafından kodlanan helikaz, virüsün yaşam döngüsünde kritik bir rol oynar ve tedavi yaklaşımlarının merkezinde yer alır. Bu çalışma, helikaz protein mutasyonlarının Amerikan SARS-CoV-2 izolatlarında protein stabilitesi ve nükleik asit bağlanma dinamikleri üzerindeki etkisini ortaya koymuştur. 2483 Amerikan izolatından tanımlanan dokuz mutasyondan (Ser36Pro, Thr127Asn, His164Tyr, Met233Ile, Tyr324Cys, Ala368Val, Ala389Val, Arg392Cys, Thr599Ile) elde edilen veriler kullanılarak, derin öğrenme algoritmaları ile mutant protein modelleri oluşturulmuştur. Protein stabilitesi değişiklikleri SDM2, mCSM, DUET ve DynaMut2 araçları kullanılarak değerlendirilmiştir. Helikaz-nükleik asit etkileşimi, moleküler kenetlenme analizi yoluyla değerlendirilmiştir. Sonuçlar, dokuz mutasyondan sekizinin genel olarak protein stabilitesinde azalmaya yol açtığını, His164Tyr mutasyonunun ise tüm değerlendirme araçlarında stabiliteyi artırdığını göstermektedir. Moleküler kenetlenme analizi, mutasyonların helikaz-nükleik asit arayüzünü enerji ve uzamsal yeniden düzenlemeler açısından değiştirdiğini ve böylece bağlanma afinitesini artırdığını ortaya koymaktadır. Özellikle, elektrostatik etkileşimlerdeki artış, nükleik asit bağlanmasının iyileştiğini düşündürmektedir. Çalışma, artan bağlanma afinitesi ile azalan protein stabilitesinin eş zamanlı olarak ortaya çıkmasının viral replikasyon hızını karmaşık bir şekilde etkileyebileceği sonucuna varmıştır. Bu bulgular, helikaz hedefli antiviral ilaçların geliştirilmesinde bölgeye özgü mutasyonların dikkate alınmasının önemini vurgulamaktadır.

Keywords

• SARS-CoV-2
• Helikaz
• Mutasyon
• Protein stabilitesi
• Bağlanma dinamiği

Supporting Institution

Malatya Turgut Özal Üniversitesi Bilimsel Araştırma Projeleri Koordinatörlüğü

Project Number

2022/13

Ethical Statement

Gerektirmiyor.

Thanks

Bu çalışma, Malatya Turgut Özal Üniversitesi Bilimsel Araştırma Projeleri Koordinatörlüğü tarafından 2022/13 numaralı hibe kapsamında desteklenmiştir.

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